Freaks of Nature
by Ulura
Summary: Sherlock meets Startrek. The super humans were not the tyrants Starfleet made them out to be, infact they were betrayed. Sherlock, John and their fellow superhumans decide to freeze themselves and wait for a better time. But when Marcus finds the ship Sherlock is forced to work for him until he dares to make an escape. Can he convince Kirk of the truth and save John and the others?
1. Chapter 1

**I know this story should technically be in the cross over section but thats a much smaller reader pool, so I put it here and also on AO3. If you enjoy please review :)**

* * *

The chase had taken it's toll on them.

They'd even lost a few along the way and the SS Botany Bay was a little worse for wear. Nothing serious, but certainly more than they were used to. Usually Sherlock reveled in the excitement and puzzle solving that was a good chase, then again, usually he was the one doing the chasing. Seventy five of them had managed to get aboard the ship before he'd been forced to take off, abandoning those few left behind to their fate.

Starfleet had pursued them of course, but Sherlock was too clever for the likes of them and they had escaped. So now here they were, floating behind some moon on the far end of the galaxy. Mycroft had just shut off their systems, leaving them completely invisible to any craft that passed by this quadrant. Not that any would, Sherlock had done the calculations, odds were nobody would find their hiding ship for hundreds of years.

"What do we do now?" Lestrade had asked when they had finally gotten settled, "Just, float through space for the rest of our unnaturally long lives?"

"Cryogenic tubes." Mycroft replied, "Enough for all seventy five of us, we'll wait out here for however long it takes for those traitors to destroy themselves and then we will find ourselves a new home in the future."

It was not a perfect plan but Sherlock had no better ideas.

Currently, seventy three of said cryotubes were activated, their occupants set to sleep for the next few hundred years. Only Sherlock and one other were still awake. Sherlock found him on the deck of the ship, watching the stars.

"It's a long time to be sleeping." John sighed.

"It will not feel so." Sherlock replied.

"I still think we should have stayed, we should have fought." John growled, not meeting Sherlock's eye, "We're smarter, stronger than them, we could have won!"

The control panel began to groan as John's grip began to crush it.

"Human's like to pretend they are God, they meant to create an army of perfect soldiers and they succeeded." Sherlock smirked, "They just didn't count on us thinking for ourselves."

The eugenics program that had seen them and their companions born began almost forty years ago now. At first it was wonderful, then Starfeet began to worry that Sherlock and his kind would rise up against them and decided it was better to strike first than be struck.

"Come, the sooner we sleep the sooner we can wake in a better time." Sherlock called, heading off the bridge and toward the cryorooms.

"Six hundred years..." John mused, stretching before climbing into the cryotube, "I'm going to have some killer bed head."

Sherlock chuckled.

"See you in six centuries." He joked darkly.

"You'll probably be late." John teased, pulling the door closed and initiating the freezing process.

Sherlock followed suit.

His last thought before falling under was to hope that when he woke up, they would indeed find themselves in a better place.

-oOo-

Just as he'd told John he felt as if he'd only just closed his eyes when once again he found them opening. He expected the room to be full of cold fog and several of his companions, John included, stretching out their sore muscle. Instead he saw a group of strangers observing him from inside an unfamiliar white room.

His mind was sluggish from years of disuse but it still took him only moments to deduce hat his cryotube had been moved and he was now under surveillance. Warily he sat up, facing the small group of scientists

"Why am I here?" He asked cooly, "Where is my ship and crew?"

"We have commandeered them." A voice replied, not from the group of scientists but from the other side of the room.

This man was clearly not a scientist, he wore a strange dark suit with a silver pin. Sherlock felt his blood boil as he studied the design, it was different but it was unmistakably Starfleet.

"Out tests show you and your crew age quite well." He continued, Sherlock could practically here John within his mind answering 'we moisturize'. Sarcasm had never been Sherlock's forte, so he kept the silent joke to himself.

"Three hundred years just floating in space, we thought you'd be grateful."

"You should have left us." Sherlock sneered, "Where are they? What have you done with them?"

"They are still safely asleep." The man answered calmly, "If you wish them to stay that way I suggest you co-operate."

-oOo-

Two years.

Two long years had passed since he'd woken. Two years under Admiral Marcus's thumb, building weapons, designing space ships in secret, being called John Harrison. He had to chuckle at the irony of being named John. Marcus, to his knowledge, did not know the name of his crew so it had been coincidence. However, if he had to choose an alias, John wasn't a bad name to go by.

He'd not left Area 31 since he'd arrived here all that time ago. He'd not been allowed to wake any of his companions, nor did he want to make friends with any of the human scum that worked there.

It had been lonely.

The Admiral explained that they had located his ship and his crew some time ago, identified them as the Augment's who'd fled nearly three hundred years ago and decided to put him to use.

Several times he'd considered escape, but he couldn't leave his crew, nor could he find a way to discreetly smuggle all seventy five of them away. He was trapped.

It had taken him a while but he'd located John, still fast asleep of course but his presence gave Sherlock some form of comfort.

"Mycroft would probably laugh at me for engaging in conversation with a frozen person." He sighed, sitting by the tubes, "You'd say it was some sort of coping mechanism, maybe you're right."

John was, for once, stubbornly silent.

"Why is it when I want you to talk you don't reply?" Sherlock sighed, "Before I could never get you to shut up. Still, better company than Anderson."

Finally, he saw an escape.

Marcus wanted torpedos, halfway through the design Sherlock realized they were roughly the same size as a cryotube. It had taken all his stealth and wit to sneak the seventy five members of his crew into the weapons but he'd done it, even managed to load them into a ship ready to flee. But of course, luck was not on his side.

Alarm bells rang and Marcus came for him, he had no choice.

Logically he knew his best chance of rescuing the rest of his strange family was to flee and then attack from the outside. It still filled his heart with guilt to hit the transport button upon the ship and disappear, leaving them all behind.

He spent the next few months planning, learning the history of the past three hundred years he'd slept through. It took time, but soon he was almost ready to attack Area 31 and take back his crew.

But Marcus beat him to it.

He'd felt his heart clench when he saw the news.

"STARFLEET USES NEW PHOTON TORPEDOS TO HOLD OFF ROMULAN ATTACK FORCE AT BETA CENTARI EIGHT."

Marcus had fired the torpedos.

The torpedos he'd made. The ones containing his friends, his family.

Mycroft, John, Molly, Ms. Hudson and so many more, all dead.

He'd promised them a new life and he'd failed, he'd lead them to their death.

John, his first officer, his doctor, his best friend, he'd killed him.

That's when Sherlock decided that Marcus was going to pay, he was going to make sure of it, even if it was the last thing he'd ever do.

* * *

**Long prologue I know!**

**IMPORTANT**

**I'm going to skip forwards now to after Pike was killed and begin when Spock, Jim and Uhura go to Chronos because up until them everything happens as it does in the film and rewriting it is a bit of a waste of time don't you think?**

**BUT if you guys really want me to I can rewrite the scenes but it will take me a while and everything will happen exactly as it did in the film, there will be no changes. **

**I finish the term in two weeks, once I finish school updates will be faster but until then they should be every 4-5 days. **


	2. Chapter 2

Kronos was a desolate place, especially the abandoned sector where he had been residing since his attack on Starfleet headquarters. He knew of the tensions between the Kligon Empire and Starfleet of course, it was the whole reason Marcus had awoken him in the first place. The area may be a huge rust pile, but Starfleet would not follow him here.

At least that's what he'd thought up until now.

He was barely paying attention to Captain Sulu when the message came through until he heard the words 'photon torpedos'.

"-So unless you want to end up like those Romulan ship's a few weeks back I suggest you comply or we will annihilate you."

Had Marcus saved some of his weapons? Knowing he'd come after them if he knew? This was probably a trap, Sherlock knew, but there was a chance, a slim chance that some of his crew was still alive.

John could still be alive.

It was worth the risk.

Quickly he shouldered the large laser turret he'd been working on and stepped outside of the small hovel that was his home. He could see several Kligon ships circling and the sound of yelling, both native and human. So Sulu had sent an away team down here? Why?

No time to ask questions, the first of a small platoon had dropped from their ship and began to charge toward him. Laser blasts took them out without a problem, he quickly dispatched the rest with a wave of the turret and hits of his own.

With a strong leap he jumped from the platform he'd been standing on down to the group where the Starfleet officers were currently fighting. Perhaps he could take one or two out by 'accident' while he shot at the Kligons, yes that would be fun.

Sherlock raised his gun, ready to fire at one of the humans who had foolishly left his back to him. His finger reached for the trigger but froze when he turned. The blonde hair and blue eyes struck a cord with him, and for a few seconds Sherlock swore it was John looking at him. A Kligon appeared behind the man and without thinking, Sherlock shot him down. The blonde man looked down at the body in shock and then back to Sherlock, his face contorted with rage and the resemblance to John was shattered.

_'Fool!'_ Sherlock mentally chided, _'Stay focused!'_

"How many torpedos?" Sherlock demanded, stalking toward the group of Starfeet officers

"Stand down!" The Vulcan ordered, Sherlock had no patience for this, he swiftly shot the gun out of his hands.

"How many!" He repeated, "In your message, how many torpedos do you have?"

A pause.

"Eight." The Vulcan replied finally.

Eight. Only eight left. Seventy five of them had been sleeping when he'd closed his eyes just over three centuries ago and now only eight remained. He knew it was illogical to hope but John could be among them. It was worth the risk.

"I surrender." Sherlock breathed, throwing down the laser turret.

The humans seemed surprised by this, the Vulcan, of course, showed nothing. His gun was picked up of course and aimed right at him though he knew they wouldn't shoot. The blonde one whose life he saved glared at him with obvious hatred. Sherlock regarded him with his usual blank gaze.

"In the name of Christopher Pike, my friend, I accept your surrender."

Sherlock had a handful of seconds to process what this meant before his face was met with the humans fist. It barely hurt of course, he was genetically designed to feel as little pain as possible, which was a good thing considering the blonde man continued to throw punches. Sherlock took them, there was no point fighting back, this tiny human was hardly going to do any lasting damage.

_'Clearly he is furious with me personally, yet we have never met. Odd. Christopher Pike, he was a Starfleet captain I recall. Ah yes, he must have died during my assault on their headquarters, probably a good friend of this man. Hence his anger at me. Simple._

The deduction took less than five seconds.

"Captain!" The woman yelled, pulling the man off Sherlock.

Ah, so this Sulu was clearly acting captain then and this blonde was really in charge, interesting. If he'd had to pick he'd have guessed the Vulcan would be captain.

"Captain." He smirked, under any normal circumstance Sherlock would be embarrassed to have been caught by such an emotional man child.

"Cuff him." The captain growled.

-oOo-

John Harrison confused them all.

Logically Jim knew that man could have beaten them all, he had the superior weapon and, judging by the beating he took without batting an eyelash, superior endurance. Yet he walked calmly along with the guards, not even trying to fight or escape the handcuffs he'd practically put on himself. One would think he _wanted_ to be captured.

"Uhura, contact Starfleet let them know we have Harrison in custody." He ordered, "Spock come with me and summon Bones to meet us in the brig."

Bones went through the usual drama of complaining about his state when he saw the blood on his clothes. Thankfully all the wounds were superficial and the trio were quickly on their way to visit their latest prisoner.

"I am concerned captain, it seems illogical for Harrison to have surrendered to us." Spock spoke up immediately.

"I know, I'm worried too." Jim replied as they walked.

"You say he took out an entire Kligon brigade?" McCoy gaped, "He sounds like a Superman."

"You're telling me." Jim breathed.

He didn't mentioned that Harrison had saved his life. For what purpose he had no idea but when he'd turned to face him Harrison had his gun trained on him, but he'd hesitated, instead of shooting he'd just looked at him for a few seconds. Then, he'd shot the Kligon that was about to end him. Why? What motive could the fugitive possibly have for saving him? A man, to his knowledge, who had been sent to kill him.

Harrison regarded them from the other side of the glass with steely eyes.

"Captain James Kirk, and officers Spock and McCoy." Jim introduced tersely.

"Why aren't we moving, captain?" He asked calmly.

Jim was usually so good at reading people but this guy...his entire face was a mask.

"Unexpected malfunction, perhaps in your warp core?" He continued when none of them answered.

How on earth did he know that? They had walked through engineering yes but, to deduce all that in a single minute while being escorted. It was impossible...

"How the hell do you know that?" Bones asked.

"I think you will find my intellect valuable, captain." Harrison replied, once again addressing Jim rather than Bones, who had actually asked the question.

Spock gave him a serious look, which after spending time with him Jim had learnt mean 'say nothing'. On another occasion he'd have listened but right now, right now he felt his blood boiling with rage. How could Harrison just stand there so complacent after ending so many lives with his bomb and attack?

"Listen very carefully." He sneered, doing his best to keep his temper under control, "You are a criminal, I watched you murder innocent men and women, I was authorized to _end_ you! The only reason you are still alive is because I am allowing it!"

"Captain are you going to punch me again, over and over?" Harrison drawled, having the audacity to sound bored.

"I surrendered because, while your temper suggest otherwise you seem to have a conscience. If you did not it would be impossible for me to convince you of the truth. 23 17 46 11, co-ordinates not far from Earth. I suggest you take a look, because then you will know why I did what I did and who knows, maybe you'll agree with my actions."

"I will never agree with what you did." Kirk spat, "Give me one good reason to trust you."

"I can give you eight, Captain. They're aboard this ship." Harrison cut back without pause, "In the past I could have given you over seventy, but no longer."

What on earth did that mean?

* * *

**This is going to be different from the film like I said, so in this Sherlock deduces Marcus's plan when he walked through engineering and saw the state of the warp core. **


	3. Chapter 3

He was going to bloody kill Jim Kirk one day. If he went prematurely grey it was his fault. He was a doctor goddammit not an engineer! He didn't know anything about taking apart torpedoes and yet, here he was a stupid moon about to disassemble one.

"Harrison told me there were eight reasons for him to trust him, all aboard this ship." Kirk had explained, "Obviously he means the torpedoes but for some reason we can't identify what's inside them. Even Carol can't figure it out with all her fancy credentials. I've sent Scotty to the co-ordinates he told me anyway but to be safe, we need to know what's inside those torpedoes."

So here he was, alone with a woman on a deserted moon and instead of what he'd always imagined, he was going to take apart a weapon.

"We need to access the war head but to do that we need to be delicate, one wrong move and this thing could arm itself and explode." Carol explained, slowly sliding the casing open, revealing a plethora of wires and tubes.

"Start with the twenty third wire down." She ordered, bossy, no wonder Jim liked her.

Not even the C-section on the pregnant Gorn could compare with the effort he was putting in dismantling this missile. Ever time he cut a wire he was ceased with the fear that it could set the explosive off, by the end of it he was sweating like a pig.

"Only one more now..." Carol breathed, "Fourth to the left, the red one."

Holding his breath, Bones cut the wire. A soft buzzing sound was emitted and all the lights and cables dimmed. They both let out a sigh of relief as the compartment above the missile opened.

"Well, Bones?" Jim's voice crackled over the com but Leonard found his mouth dropping open in shock, unable to reply. He'd been expecting some sort of new core or armed fuel, not what they found.

A body.

There was a man inside the missile, frozen inside a cryotube. Obviously still alive, but in cryogenic sleep. Suddenly, he remembered the assault on the Romulan's only a few weeks ago, they'd used over sixty missiles just like this one here in the attack. Had there been people in those as well?

What the hell was Harrison playing at?!

-oOo-

"Why would somebody remove the fuel component and place a cryotube inside?" Kirk wondered allowed when he appeared in the medical bay.

"No idea but all eight of them are exactly the same." Bones replied, clearly baffled, "Jim, you don't think the torpedos used in that defensive maneuver agains the Romulans..."

Bones trailed off but his intent was clear, to be honest Kirk was wondering the same thing.

"We have five men and three women," Spock noted, taking in the cryotubes.

"Can we wake them?" Kirk asked but Bones shook his head.

"Not without the proper sequencing, it would kill them. This technology is beyond me."

"How advanced?" Spock cut in.

"Quite the opposite, these tubes are ancient." Carol replied, "These people, they're three hundred years old."

-oOo-

"What are you playing at?" Kirk demanded, finding himself glaring once more at Harrison's unfeeling face. Just looking at him made the anger grow.

"Why is there a man in that missile!?"

He wasn't sure but for a second, Jim was sure he saw relief flash across the fugitives face.

"He is there because I put him there." Harrison replied, he sounded, regretful?

"It was a plan, to smuggle them all to safety." He continued, "But I was caught and your Starfleet fired them at their enemies knowing full well my family laid inside them."

Family?

"That is why you attacked the Starfleet headquarters." Spock deduced in his usual calm manner, "Revenge for the loss of those sixty seven lives."

Harrison nodded.

For a moment, Jim felt sympathy for the man inside the cell, but then he remembered finding Pike's body and he soon forgot it.

"Who the hell are you?" He asked, unable to keep the venom from his voice.

"A relic, created by your Starfleet over three centuries ago. Genetically altered to be superior in strength and intelligence so to lead the world into an era of peace." Harrison explained sounding mournful, "But we were betrayed, turned on by the very ones who'd created us and forced to flee, forced to exile ourselves in the deepest realm of space."

"We had planned to sleep for longer, but as a result of the destruction of Vulcan your Starfleet began to explore deeper realms of space and we were discovered. I alone was revived by your Admiral Marcus."

He stopped then, looking at his hands before curling them into fists.

"I was kept, prisoner. Forced to build weapons, design ships for a militarized Starfleet in exchange for the lives of my crew. I tried to smuggle them to safety in the weapons I'd created, but the plan was foiled and I was forced to escape alone."

"And in return Marcus killed 90% of your crew." Spock concluded, Harrison nodded.

This was ludicrous.

"Admiral Marcus wouldn't do that." Kirk argued, "Why would he ask a three hundred year old frozen man for help?"

"Because I am better." Harrison glowered, "At everything. My mind is superior to yours in every way, I can create ships and machines you could never dream of. And I did. Now, he wants to start a war, the war he's been dreaming of for years, he sent you here to fire the last of my people at the Kligons and then stranded you here via a breech in your warp core."

"You expect us to believe this?" Kirk yelled, "You are a liar and a criminal."

"I did what I had to! Marcus took my friends from me, used them to control me!" Harrison burst, anger and pain showing on his face for the first time, "My crew is my family, the only ones like me to ever exist. Is there any thing you would not do for your family?"

Kirk watched emotionlessly as he saw unshed tears forming in the man's eyes.

"Marcus murdered those who I held most dear, those eight, I do not even know which eight, are the only ones left. The only ones left who know and understand me, the only ones who know my name." He breathed, "I will not allow you to take them from me as the admiral took the others."

The two glared at one another for a short while, Spock remained unusually silent. Jim still felt anger, immense anger for the loss of Pike, but when he looked in Harrison's eyes, he saw no deception.

"What is your name?" Spock asked finally, "John Harrison is clearly an alias, I assume given by the Admiral."

"My name..." He breathed, "Is Sherlock. But I haven't not been known by it for many years now."

The strong warrior with the emotionless mask was almost gone now, Harris-Sherlock, seemed very human all of a sudden.

"Why didn't you kill me?" He asked finally, "On the Kligon home world, you had your gun trained on me and you hesitated when you saw my face."

Sherlock regarded him.

"All those centuries ago I too was a captain and I had a first officer, a doctor." He replied, not meeting Kirk's eye, "John, my greatest friend. My brother, who is more than likely now scattered across space as dust. You...remind me of him."

Jim had not been expecting that.

The reverie was broken when the sound of Sulu came across the com.

"Sir, there is a ship approaching us at warp."

"Marcus..." Sherlock hissed, "I knew he would come."

* * *

**Woo, things can finally start really changing from the movie story line now! **


	4. Chapter 4

Sherlock's words echoed through Jim's head as he made his way to the bridge.

"Sherlock showed none of the signs of lying." Spock ensured him, "What he says, at least to his mind is true. As far as I can tell."

"Just because his twisted mind believes it doesn't make it true, maybe he is just a good liar." Kirk argued.

"That is also true." Spock replied, "I do not have sufficient data to-"

"Not now Spock." Jim sighed, "I don't have the patience to listen to number crunching we have bigger issues."

The two made it out onto the bridge just in time to see the largest ship Jim had ever seen appear before them. It was colossal, three times the size of the Enterprise and black as night. Though he could clearly see from the design that it was a Starfleet ship the captain couldn't help but feel uneasy. There was something, off, about it. Specifically the large number of weapons he could see located about the hull.

"We're being hailed sir," Uhura announced as he took his seat, "It's the Admiral."

"On screen."

The Admiral's face digitally appeared before him but something was different now. When he'd last seen the Admiral his face was trustworthy, a relief. Now, even though he knew deep down nothing had changed, the face seemed secretly hostile. He couldn't help but notice that the large warship, there was no other name for it, did indeed seem to back up Sherlock's story.

"Captan," He greeted.

"Admiral, we weren't expecting you." Jim replied warily.

"Yes, well I was equally surprised when I heard that instead of killing Harrison as ordered you captured him." Marcus replied, he sounded too calm...

"Yes, we had a breach in our warp core and didn't want to risk being caught firing weapons."

"Understandable, since you have Harrison in custody simply beam him over to us, I'll take him back to Starfleet headquarters." Marcus continued smoothly, "Then I'll beam over some engineers to help with your repairs."

_Why would he wait until after to send help? _Jim thought to himself, he loathed to admit it, but Sherlock's story was making more and more sense.

"Of course, Sh-Harrison is, in the holding cells. I'll send him over momentarily." He said carefully, "Kirk out."

He quickly signed off the video message before Marcus could notice he'd almost called Sherlock by his real name. So many times he'd followed his guts instead of obeying orders and things had always paid off for him. But right now his gut was telling him Sherlock was telling the truth and that Marcus, a man he'd looked up to, was a lying scoundrel. That's not what he wanted to believe.

"Send word to the holding cells and have Sherlock taken to the medical bay." He ordered, jumping out of his chair once more, "Spock you're with me, Sulu you have the con."

-oOo-

"You want to what?" McCoy demanded.

"Wake the rest of these people up." Jim repeated, "With Sherlock's help you will be able to get the sequencing correct."

"So you really believe that story he told?" McCoy scoffed, "You can't be serious!"

"On the contrary, Doctor." Spock cut in, "All signs show that there is a 68.9% chance that Sherlock's story is true."

"Only 68.9%?" McCoy teased.

"I do not have sufficient data to-"

"Not now you two." Jim sighed.

Couldn't they ever be in the same room without bickering? Not that Spock would call it bickering, he'd probably call it a debate.

"Though I must say captain, I too have reservations about waking more of Sherlock's crew up." Spock argued, "We were not able to fight him alone, together they could easily take control of this ship."

They had a point...

"You wanted to see me, captain?"

How is it that Sherlock managed to always say his title as if addressing a child playing dress up?

"I just spoke with the Admiral." Jim informed him.

"Let me guess, he offered to send you help to fix your warp core, but only after transporting me to his ship." Sherlock drawled, "It is the most likely scenario I can imagine after observing your behavior earlier."

Damn that smug bastard.

"One would think you'd be thankful we've unlocked you." Jim ground out.

"And placed me in the custody of several security guards." Sherlock eyed the red shirts with content, no doubt he could take them down if he really wanted to.

Suddenly it occurred to him that in a way, despite his hostile demeanor Sherlock was actually being quite tame. Jim had seen him take out an entire Kligon patrol without breaking a sweat, so taking out several security guards and taking over the ship wouldn't be a trial for him.

Jim's eyes slid over to the cryotube that had been removed from the torpedo resting on the medical bench.

_He's here for them. _He thought to himself, _he only surrendered after he found out we had his missiles._

**_"Is there any thing you would not do for your family?"_**

"Give Doctor McCoy the sequencing to open the cryotube safely." Kirk ordered him, without meeting his eyes.

He felt a small amount of smugness when Sherlock was unable to hide his surprise for a few short moments.

"Why are you allowing me to do this?" He asked, pale eyes finding the captain.

"Because, if your story is true," Jim answered slowly, "Then we are on the same side."

"**If**" McCoy repeated.

Sherlock regarded them warily but said nothing as several of engineering's men bought up the remaining cryotubes. It took quite some time, seeings as Carol had to transport down and disarm every single one individually. Finally all eight were laid out on beds from the sickbay like little metal cocoons.

"Pick one then." McCoy ordered gruffly, "Then give me the sequencing."

Sherlock looked over all the numbers on the pods, finally settling on the one McCoy had helped disarm first. It took several minutes for the man to explain to the doctor how to open the pods much to his frustration.

"Just allow me to do it myself! One wrong number and you could potentially kill them." Sherlock argued but McCoy, as usual, was stubborn.

The entire time he'd been aboard Sherlock had been, calm, collected and somewhat smug. Now, while his mask was still in place, Jim was sure he could see a multitude of emotions swirling in those grey eyes.

Finally the frost melted, clearing the small window inside the tube and the latch clicked. With a groan the man inside sat up and stretched before taking in his surroundings. Though he only had Sherlock's brief description to go on Jim was sure this was the John he'd been talking about. Blonde hair, blue eyes, he looked a little older but Jim could defiantly see the similarities.

"John." Sherlock greeted, his voice seemed cold, especially after all that had happened, but there was a trace of a smile.

Jim didn't know what he was expecting, certainly not tearful hugs even he could tell Sherlock wasn't that sort of person, but certainly more than just a name. Though he did notice the stiffness that had surrounded the super human was dissipated slightly in the company of his comrade.

"Should have known you'd be first awake." John grinned, "Who are these people?"

"No need to worry," Sherlock insisted before fixing his eyes on Kirk, "These are our allies."

"Allies?" John quested, getting to his feet, "Since when are we allies of Starfleet?"

"It is a story for later," Sherlock dismissed, "Meet Captain Kirk, Doctor McCoy and Mr. Spock."

"Right..."

"Nice to meet you?" Jim tried, offering his hand, John moved to take it but stopped when he saw Sherlock's face.

"I'm guessing I'm missing something as usual." John replied seriously before rotating his left shoulder, "I'll have to get Sarah to look at this arm, being frozen for a few hundred years really stiffens old wounds."

Sherlock stiffened. Jim could guess why.

"John, Sarah isn't here." He said finally, "These few tubes you see, that's all that's left of us."

"What!?"

It was awkward, standing by and having Sherlock explain his story once more, a little more gently this time. Spock, being Spock, cut in a few times with extra details after the Enterprise came in but McCoy swiftly shut him up. By the time Sherlock's story had caught up with the present, John's hands had been balled into fists.

"So," He growled, "Who is left?"

"If I'm remembering the numbers correctly-"

"You are." John smirked.

"Then Lestrade, Irene, Mycroft, Molly, Anderson, Donovan and Moriarty are still alive." Sherlock listed, "That's if they all went to their assigned pods."

John sighed mournfully.

"So Sarah? Ms. Hudson? Dimmock?"

"All of them." Sherlock nodded, looking guilty.

"I know it's no consolation," Jim spoke up finally, "But I'm sorry that happened to your friends, your family."

"Starfleet apologies mean very little to me." John glowered.

"Do try not to punch a hole in the ships hull, you remember the trouble that caused the first time." Sherlock drawled, "I dislike it as much as you but you know the saying the enemy of my enemy is my friend."

"I have no interest in befriending this lot." John snorted, going to investigate the other still frozen members of their crew.

McCoy glared right back, obviously just holding back his usual sharp words.

Sherlock chuckled slightly, it as the first time Jim had heard such a sound from him.

"If you thought my temper was bad, just wait and see how bad John's is."

* * *

**Duh! I can't believe you guys thought I'd kill of John so early :P **


	5. Chapter 5

**Important Characterization Note!**

**Quite a few people have been commenting on how strangely I've written characters, specifically John and Sherlock so I just thought I'd explain my reasoning. Firstly, I've combined elements of Khan into Sherlock, so he is like 10% Star Trek Villain. As for the defensiveness and anger both John and Sherlock display I think about it like this, to them Starfleet are the people that controlled and created them for their own purposes only to turn on them and try to kill them later. Then, force Sherlock to build weapons while keeping the rest hostage before finally killing 90% of their friends/family. Hence why John distrusts Starfleet officers so much, at least for now :P Plus we all know John goes BAMF when people he cares about are in danger so I'd expect he'd be pretty bitter that most of his friends were killed. **

* * *

Sherlock was furious when they refused to allow him to wake the remaining members of his crew. Jim had no doubt that he'd have fought them for it had they not been inside the medical bay itself. Maybe it wasn't in the traditional sense but even Jim could see he cared for the people inside the tubes.

"Why are we trusting these people?" He heard John hiss, "They're Starfleet, how do we know they're not in league with this, Admiral Marcus you told me about?"

"I am not sure about the rest of the crew, but the captain can be trusted, at least minimally for now." Sherlock assured him, "Kirk will not fight us. At least, not unless we give him a reason to."

"It's not like you to trust people so easily."

Jim almost revealed himself then when he almost scoffed out loud. This is what John referred to as trusting easily?

"He reminds me of you when we first met." Sherlock admitted which made John laugh.

"I almost took your head off in the training arena."

"Well, different place same action."

"I believe we should focus on the issue at hand." Spock spoke up, "No doubt the Admiral will be starting to suspect all is not as it seems as Sherlock has not been transported aboard his ship as he ordered."

"I say we wake the rest of our friends and transport aboard, Sherlock designed the ship, he can take it out." John suggested.

"And what? Kill his entire crew?" McCow scowled, "Even if Marcus is dirty that doesn't give us the right to end dozens upon dozens of lives."

"Never stopped you in the past." John replied.

"Now is not that time, John." Sherlock sighed, "What's done is done, getting angry at the doctor will not bring them back."

"Don't be a hypocrite!" Kirk snapped, "You murdered all those members of Starfleet when you attacked our headquarters!"

"At least he killed people who deserved it."

"Why you-!"

"Gentleman! Arguing amongst ourselves wont solve anything." Spock cut in.

John and Jim continued to fume at one another with hard eyes. Yes, he could definitely see the resemblance.

"I must get aboard the Admirals ship." Sherlock started, "A small group would be best, I would suggest just John and myself but no doubt you would take issue with that."

"For good reason." McCoy smirked, Sherlock glared at him.

"In that case I would recommend adding Captain Kirk and his first officer to join us."

That was surprising.

"Clearly you are both accustom to working together," Sherlock explained, "And you are also the highest rank on this ship and have connections with the Admiral, you are the obvious choices."

Kirk gave him a nod.

"So, how do we get on board the ship?"

Sherlock immediately began to rattle of his plan at lightning speed, Jim almost had trouble keeping up. But after a little while he found himself grinning, if the situation weren't so dire the plan would almost seem fun.

-oOo-

"Are you sure I have to wear this?" John asked, stretching the collar of the security uniform, "Wearing so much red makes me feel like a giant target."

"Security personnel wear red in Starfleet." Spock replied curtly, "If you are to pass as Sherlock's escort you must be dressed appropriately."

"I'd still feel more comfortable if one of us was going with you." McCoy mused.

To be honest, so did Jim but Sherlock had been perfectly clear on the plan. Marcus had never seen any of the other people within the pods, so John was the only member of the group he wouldn't recognize. The two super humans would beam aboard and take out any and all people within the transport room before sending word to the Enterprise and beaming over Jim and Spock.

Jim just prayed they did as they said they would, rather than tear the new war ship apart from the inside out.

"Remember, try not to kill unless it's absolutely necessary." Jim warned them, to his surprise John gave him a firm nod.

"I'm a doctor before a solider," He assured them, "I always try to keep my kill count under my saved and I will keep an eye on Sherlock as well."

Some how Jim knew that wasn't some lie spun to make him feel better.

"We shall be expecting your message within the next four to seven minutes." Spock announced, readying the transporter, "Engage."

-oOo-

It was almost like old times. Sherlock felt an energy he hadn't since he'd been awoken in this dull future, suddenly the idea of a mission excited him. He and John had been partners on almost every job, every flight and every trip since their creation, they were the perfect fighting pair. He felt as if he'd been missing a limb since Marcus woke him, while part of him still felt hollow at the idea of so many deaths, John made him feel considerably better.

Foolishly, Marcus himself was not present in the transport room. There were several security personal though, not that it could stop him. His wrists easily slid free of the unlocked cuffs that had been resting against his wrists. The sound of crushing bone as his fist made contact with the first man's nose was extremely satisfying.

It took them only four minutes to knock out all the guards as well as the transporter worker. They could have done in half the time were they permitted to kill. Sherlock wished they could have, not because he enjoyed the taking of life needlessly, but because it would have been faster.

John looked to Sherlock and then to the door, the intent was clear.

Do they follow through and transport the Vulcan and captain aboard, or do they go off on their own like so many times before?

Sherlock hit the transporter key.

"You trust them?" John questioned, Sherlock nodded.

"When I attacked the Starfleet Headquarters I killed a good friend of the captain and yet he still listened to me." Sherlock explained, "I believe he can be trusted and the Vulcan will follow his every order."

John nodded and gave him a small smile.

_'I'm with you.' _

The two figured faded into view and stepped off the platform.

"Had us worried there for a minute." The captain half joked.

"We need to get to the bridge." Sherlock ordered, getting straight to the point, "I designed this ship to be run on a minimal crew, one if necessary, Marcus would not want many people knowing about it yet."

"So you think it's possible to get to the bridge without setting off any alarms?" Kirk questioned.

"If we're careful." John nodded, "Let's go."

As they had predicted the corridors were empty, Sherlock theorized that despite the ships size, there was probably only fifty or so crewmen aboard. Half of which would be in the engine rooms and the other on the bridge.

"Security!"

Sherlock hated when he was wrong.

"Dammit!" John hissed as several guards appeared around the corner brandishing phasers that were definitely not set to stun.

It seemed Kirk and Spock were just as accustom working together and John and himself as both dodged without batting an eyelid. Taking out the first few was easy but then Sherlock felt the painful sting of a phaser hitting his back, even when set to kill it wouldn't hurt him too badly of course but it did knock him down.

He turned, ready to fight only to see the gun right in his face with it's trigger about to be pulled. John was on the other end of the room and Kirk and Spock were too busy with their own enemies.

CLANG!

The man holding the gun slumped and hit the ground as a large metal container from a nearby work bench slammed into his head. Without hesitating Sherlock grabbed the phaser and swiftly dispatched the remaining members of the security team before turning to see who had saved them.

"Honestly, I leave you unattended for two years and you build a battle ship." Lestrade sighed, stepping out from the shadows.

"What on Earth am I going to do with you Sherlock?"

* * *

**I picture Lestrade as a sort of fatherly member of the group :P When I watch the last scene in a study in pink when Sherlock is wearing the blanket and Lestrade says "Yeah but some of the guys want to take photographs" I can just imagine Sherlock whining "But daaaaaaaaaad" :P**


	6. Chapter 6

"Lestrade!" John exclaimed with a wide smile, "How on earth did you get here?"

"How indeed." Spock remarked as he relinquished the now unconscious men of their weapons.

"Well, somebody had to wake up every few decades to make sure the ship was still functioning properly and all the pods were still safe." Lestrade remarked, "I knew it may as well be me. Though I must admit, I was expecting to wake up on the Botany Bay again, not in some futuristic med bay with a very angry shouty man."

"That'll be McCoy." Jim grinned, he could just imagine McCoy's face.

"Well, it took a few minutes to find out what was happening but I figured I'd best get over here and help you right in the nick of time like I always do." Lestrade sighed.

"It's good to see you." John clamped a hand down on the silver haired man's shoulder, "But we can catch up later."

"That would be best, if we continue to leave bodies laying about the ship, even with a minimal crew somebody is going to start noticing." Spock spoke up, "Come we need to keep moving."

Unlike John and Sherlock, this Lestrade didn't seem at odds with either him or Spock. He didn't seem bitter at all which made Jim wonder just how much of the story McCoy revealed to him. Did he know most of his friends had been murdered?

They ran into another few security guards as they neared the bridge but John took care of them without a hitch. In fact, he slammed one into the wall so hard he dented the metal.

They stormed the bridge, the three super humans were practically blurs, taking out the men with their bare hands while he and Spock simply stunned those who remained. And there was Marcus, sitting in the command chair looking furious. All this time a small part of Jim had hoped Sherlock was wrong, that Marcus wasn't trying to turn Starfleet into an army and that this was all some misunderstanding.

Sherlock leapt for the man, no doubt ready to end him.

"Sherlock, Don't!" Jim cried, "If we kill him we have no proof!"

This didn't stop him though but just as he reached the edge of Marcus's chair a bright light descended from the ceiling, trapping Sherlock in a small cylinder shaped force field. More of them descending only seconds later, trapping the rest of them.

"Individually generated fore field cells?" Sherlock exclaimed, looking surprised for the first time, "I didn't design these, and you couldn't possibly-"

"You really think I did suspect something?" Marcus laughed, "I knew the minute the message from the Enterprise came in stating that you were alive and on board."

"How could you do this?" Jim asked, banging his fist against the glowing containment field, "How could you kill all those people? Set us up to start a war!"

"I'll admit sacrificing Starfleet's golden boy was a tough choice, but you're too kind to be a solider Kirk." Marcus smiled.

"How did you make these cells?" Sherlock demanded, as John tried unsuccessfully to break out of his.

Marcus regarded him with a superior smile. Kirk couldn't believe he never saw the darkness in that man's eyes before.

"It was obvious from the start you were going to make a run for it at some point, so I started waking up other members of your crew to find somebody...like minded." Marcus explained, "Most of them were like you, so I had them refrozen and made sure they were the first fired at the Romulans."

"You bastard!" John growled, "You utter bastard!"

"It's rude to interrupt people." Marcus glowered, pressing down on one of the buttons on the chair's arms.

A bright forked beam, like lightning, appeared over the superhuman, striking him in the forehead for several painful seconds before stopping and John slumped to the ground unconscious.

"John!" Sherlock screamed, ramming himself against the containment field so hard it actually sparked but id not fade.

"Oh, one of yours is he?" Marcus smirked, "Should have known."

"Who designed these for you." Sherlock glowered.

"A like minded member of your crew." Marcus replied.

Spock and Jim looked to Sherlock for some clue as to who amongst his crew Marcus was talking about but it wasn't needed. The doors opened and in waltz a man with the biggest grin Jim had ever seen on his face.

"Well if it isn't Sherlock and his dog Johnny boy!" The man grinned.

"Moriarty..." Sherlock glowered, "But you pod is back on the ship..."

"Quite empty you'll find." The man, who must have been Moriarty, replied, "I've been up and about going on a year now."

"You traitor." Lestrade hissed, "After all the things we've been through together, you just let this monster kill our family?"

So he did know.

"I never was one for bonding." Moriarty mused.

"What do you have planned for us now?" Spock asked in his usual calm manner, "Trapping us on your bridge full of unconscious workers seems slightly redundant."

"Oh we can easily knock you out with the concentrated beam just as we did you're silent friend there." Marcus smiled, indicating to John who was still not showing any signs of waking.

"Well, I can." Moriarty cut in, his face suddenly turning predatory.

Jim realized at the last second that Moriarty wasn't loyal to Marcus just as the super human pounced on the man, gripping his head between his palms.

"I was going to wait until after you'd started to the war to kill you Marcus, but I think you've become redundant already."

"But-" Marcus's looked fearful for the first time, "But you-"

Jim looked to Sherlock and Lestrade who, for the first time since they were trapped, were making no effort to break out.

"You bought this on yourself." Lestrade hissed.

"You should have let us sleep." Sherlock added.

Moriarty squeezed and Jim turned away at the sickening sound of bone cracking and brains and flesh spilling. He did his best not to gag, glad the containment field kept the smell of blood away from him. He looked back, purposefully avoiding the body on the flood with a bloody mess where the head should have been and focused on Moriarty. The man was shaking the red off his hands like a normal person would water.

"Should I be impressed?" Sherlock asked, hardly looking fazed at all, "You never liked getting your hands dirty."

"One must have a some fun now and then." Moriarty smiled, "Now, who do we have here? I'm assuming you're Kirk and you're his crewman."

Jim and Spock said nothing.

"Oh come come, no need to be shy." Moriarty purred.

"You'll get nothing from them." Sherlock replied instead.

"Oh, suddenly you're so confident in Starfleet?" Moriarty questioned.

"No, I saw the Vulcan activate his communicator several minutes ago which means that we should be transporting out of here and second." Sherlock replied smugly.

Spock gave him a raised eye brow which Jim knew was his way of showing that he was impressed.

"Wha-"

Moriarty didn't even get a chance to finish his surprise sentence before the silver coils of the transporter beam descended on all of them inside their small prisons.

"Terribly sorry, got to dash!" Lestrade called before the war ships deck faded and was replaced with the transporter room on the Enterprise. Jim breathed a sigh of relief and shot Spock a grateful look.

"John."

Sherlock was at the man's side, inspecting the burn mark left from the electrical shock.

"Is he alright?" Lestrade asked worriedly, "It takes a lot to knock him out for so long."

"We can take him to sickbay." Kirk offered, "But Sherlock, we need you to fix the warp core before Moriarty activates all the weapons on that ship and blows us to pieces."

Sherlock looked conflicted, Jim couldn't decided if it was because he didn't want to work with Starfleet or because he didn't want to leave John.

"Lestrade, take John and wake Anderson and Donovan," Sherlock ordered, "They may be dull but they are engineers and I will need their fast hands."

Lestrade nodded.

"We should go to the bridge captain," Spock suggested, "And be ready to warp as soon as possible."


	7. Chapter 7

"Anderson and Donovan were specially designed to work as engineers." Lestrade had explained as he input the sequence into the two cryotubes, "They've never really seen eye to eye with Sherlock but they understand that he's in charge."

"But, they've been asleep for three hundred years, engineering has changed drastically since then." McCoy argued.

"If you give me a data pad with all the highlights and important changes in the last three hundred years they can review it." Lestrade told them, prompting Spock to prepare the aid.

Kirk hadn't stuck around after that, he needed to get in contact with Moriarty and stall.

"Ready the ship to warp." Kirk ordered, "The engine will be fixed soon, we need to be ready to move the second we get the sign from engineering."

"Somebody's hailing us sir." Uhura spoke up worriedly.

"On screen."

The grinning face of Moriarty filled the window.

"Running away are we captain?"

'I just need to stall.' Kirk thought, biting his lip, 'just stall until Sherlock and his crew fix the warp drive.'

-oOo-

Sherlock was glad to see info pads in the hands of his two engineers when they arrived. At least he wouldn't have to explain how technology had evolved over he past three hundred years. He'd never been fond of Anderson nor Donovan, of the people he wished to survive they would not have made the list. But at least when things got serious they were able to handle orders with the bare minimum of sarcastic remarks and scathing comments.

"The engines been compromised, but I haven't figure out how yet." Sherlock explained and the two began eyeing over the structure looking for the problem.

"There is something wrong with the warp core." Anderson groaned, "Give me a second."

Sherlock resisted the urge to roll his eyes and the man began to re-read the data. Why couldn't he have a photographic memory like he did?

"It's out of balance." Donovan cut in, "Somebody needs to go in there and reconnect the flow of energy. But doing so will flood the entire chamber with radiation."

Sherlock growled with frustration. Making super humans had not been a cheap nor easy process, they had been allocated talents and skills according to what they were going to be. Donovan and Anderson possessed amazing initiative and skill in machinery and weapons development at the cost of their endurance and physical strength. They were still above and beyond a normal human of course but Sherlock highly doubted they would survive radiation poisoning. Their cells reproduced and healed them at an excellent rate but such damage would probably be too much for them.

Him on the other hand...he had a chance at survival. a 60% chance if his calculations were correct, his cells healed and reproduced much faster, he'd be out of commission for several days though, before he'd be fully healed.

But he'd have a better chance than his engineers.

"Is everything else fixed?" He asked, watching as the two finished the repairs at four times the normal human speed.

"Yes, all but the core alignment."

"Donovan, go to the sick bay, check on John and wake Mycroft, Irene and Molly. Tell Mycroft he's in charge until I'm fully healed." Sherlock ordered, "I'm going to need Molly's medical help if John is still unconscious. Anderson, the second the core is realigned you'll know, send word to the bridge."

They nodded, of course they didn't argue. He knew deep down they always wished Lestrade was the one who was in charge.

Focusing, he turned to the small door made of thick plexiglass that lead to the core chamber. This was not going to be pleasant. Quickly he sealed the door behind him and climbed his way through the narrow piping up to the chamber, there was no lighting but the electricity sparking from the main chamber up ahead as well as his own spectacular night vision was more than enough.

When he made his way up the large platform he could see the two diodes, the bottom one bent sideways stopping the flow of energy. For a few moments he stopped to observe, taking it all in. This technology was indeed very impressive compared to that of three hundred years ago, perhaps after all this they could fit the Botany Bay with one.

'Focus Sherlock.' He chided.

When he reached the diodes he could already feel the heat from the malfunctioning core on his skin, though it wasn't even operational. He braced his arms against the metal machinery and readier himself to push it back into place, when he did, the entire chamber would be flooded with high levels of radiations as well as bright light. To avoid being blinded he closed his eyes and with a deep breath pushed the diode forward.

-oOo-

John groaned as he swam back to consciousness. His head pounded terribly, that must have been some lighting bolt to cause such damage. He opened his eyes to find himself in the same med bay where he'd woken up a few hours ago. Some how they'd made it back.

"Good to see you awake." Lestrade greeted, pulling him to the sitting position.

"What happened, where's Moriarty? Sherlock?"

Lestrade was just finishing the explanation when Anderson arrived and started waking the last of their crew.

"Sherlock's going to realign the core." He explained, "We're going to need the med bays help."

"What do you mean?" John glowered, if Sherlock was going to do something stupid...

"He'll be in the chamber when the core realigns, it will be flooded with radiation." Anderson deadpanned.

"What!?" Lestrade demanded, pushing the engineer up against the wall, "And you just let him? We're not designed to survive a close proximity blast of radiation! Even Sherlock would struggle to heal from that!"

"We need to stop him-" John started when suddenly the damaged Enterprise gave a jolt and suddenly shifted into warp.

John felt himself pale. He was too late.

-oOo-

The second it aligned the core burst back to full power, sending Sherlock flying with the force of the shockwave, hard against the metal wall and tumbling down the tunnel. His skin burned and he could feel most that had been uncovered blistering badly. It was agony, but somehow he made it back to the door and collapsed beside it.

-oOo-

Turns out stalling Moriarty wasn't too difficult, the man clearly liked to play with his intended victims and hear his own voice. Still, it felt like a millennia had past before a strange voice, probably one of Sherlock's crew, with the simple word "go".

"Warp!" Jim ordered, not even bothering to cut off the call with Moriarty.

"What you can't-"

He never did hear the end of that sentence as the call cut off as they hit warp. Sulu had aimed the ship back at Earth, hopefully they could get back and land, explain everything and then focus on fighting Moriarty off. For the first time in what felt like an age Jim breathed a sigh of relief. He reached over to press the intercom button and thank Sherlock's crew but McCoy beat him to it.

_"Jim, John's woken up and gone down to engineering, Sherlock's done something stupid you'd better meet us down there."_

* * *

**So I sorted the super humans into categories**

**Anderson & Donovan - Engineers, not as strong or smart as warriors but have a knack for building and repairs at super human speed.**

**Moriarty, Lestrade, Irene & Sherlock - Warriors, strong, fast and cunning.**

**John - Feild medic, as strong as warriors but with medical training.**

**Molly- Medic**

**Mycroft - Analyst, the smarted and quickest of mind, but not as strong or fast as the warriors.**


	8. Chapter 8

John hated the fact that he knew very little about the layout of the Enterprise. With his speed he could get to Sherlock within a minute if he wanted to, but he had no idea which way engineering was. He had no choice but to follow Doctor McCoy at a ridiculously slow run. Lestrade stayed back with Anderson to yell at him some more and wake Molly, Mycroft and Irene.

They were about to reach the main engineering room when John slammed into something, knocking him to the ground. The something, turned out to be Kirk, who was also sprawled on the ground and quite winded after hitting John.

Normally John would have said something but right now his thoughts were with Sherlock.

"Main engineering's just through here-"

McCoy may have said something else after that but John didn't catch it, he was running toward the glass door where Donovan was standing, watching numbers on a screen and ignoring the person slumped on the door frame.

"Sherlock!"

Before he knew it he was down on his knees, pressing against the glass, trying to get passed the thing keeping him from the best friend he'd ever had. He was vaguely aware that Kirk was kneeling jus behind him but he ignored the man, his doctor's mind was taking in Sherlock's injuries and trying to figure out if he'd live.

His eyes were glazed and badly bloodshot, his skin was blistered and burnt at various points, he could tell some of his black curls had been singed clean off.

"Open it." Kirk ordered.

"The decontamination is not complete you'd float the whole area." Donovan replied, at least she had the decency to sound regretful.

"Sherlock?" John called gently, relieved when Sherlock raised his head a little, he wasn't dead yet.

"It worked then." He rasped.

"You saved us." John smiled, flicking his eyes to Kirk for a moment, "All of us. You Sherlock, you saved an entire ship of Starfleet officers. I never thought I'd see the day."

"Thank you." Kirk added.

"You'd have done it yourself, had you been here. Either of you." Sherlock replied, trying to sit up properly but failing.

"You'll be fine." John implored, trying to make himself believe it at the same time.

Sherlock tried to smile but coughed and blood spattered across his lips, John wished he could do something. He'd never felt so useless.

"I may have...underestimated just how strong the radiation would be." Sherlock continued weakly.

"Your cells will regenerate." John argued, "You'll rest, regenerate, I promise."

"Always so sentimental..."

John let out a breath that was half laugh half sob. He wouldn't let Sherlock die like this, he just wouldn't.

"How much longer until we can open the door?" Kirk demanded.

"A few more seconds..." Donovan muttered, watching the numbers and charts on the screen begin to level.

John pressed his palms against the glass even harder, trying to will it away. Weakly, Sherlock pressed his own hand against the glass where John's was resting, almost like he was trying to do the same thing.

"I'm glad you're here, John." Sherlock whispered, before his hand went lax and slid down onto the ground.

"Sherlock? Sherlock!"

-oOo-

Kirk felt guilt radiate off him when Sherlock went still, John was practically clawing at the door trying to open it. Finally, the woman gave the all clear and it slid open. The medic scrambled, lifting Sherlock gently outside the frame and gathering him up before checking his pulse.

"He's still alive." John breathed, blinking back tears he'd later deny the existence of.

"For how long?" McCoy added darkly, John glared at him.

"His cells are working overtime to heal him, but I can help." John said, getting to his feet with Sherlock's arm thrown hastily around his shoulder.

They had only taken a few steps before the ship shook and almost sent them all onto the ground once more.

'What's going on?" McCoy bellowed, "That felt like a missile!"

Another shake.

"It must be Moriarty!" John growled through his teeth, "You're going to have to deal with this one Kirk."

"But how could he follow us at warp?" McCoy asked, looping Sherlock's other arm around his own shoulder to help carry him to med bay.

"Sherlock designed that ship and Moriarty modified it, it could be capable of anything!"

_"Captain, there are two members of Sherlock's crew on the bridge demanding they take over our stations." _Spock's voice came through the con.

"That'll be Mycroft and Irene, they're annoying as hell but if anybody could out wit Moriarty it'd be those two." John grinned, "Go, I'll take care of Sherlock."

-oOo-

A ship that could follow them at warp, it was unheard of. The tremors that echoed about the ship every few seconds proved it though, they were being fired upon.

He stumbled out onto the bridge as yet another hit landed. Spock was giving out orders calmly as usual, not seeming the least bit phased by the blasts. Two strangers, who he took to be Irene and Mycroft stood by him arguing different tactics.

"Captain." Spock greeted, if he didn't know any better Kirk would have thought he heard relief in the Vulcan's voice.

"We need to exit warp." A tall man, heavily built with thinning hair told him.

"Mycroft I take it?" Kirk guessed, "Why?"

"Moriarty is behind us, if we stop he may over shoot and give us time to fire upon him." The beautiful woman with the black hair explained.

"Halt warp!" Kirk ordered without question, for a few seconds he marveled at his trust in Sherlock's crew. Only a few hours ago he didn't trust Sherlock himself, now he was following the advice of his friends without hesitation.

The ship came to a halt so suddenly Sulu was almost thrown over the edge of his console, but as predicted the large black ship shot off into the distance.

"We'll only have a few minutes until he comes back." Kirk told them, "We need to cripple his ship somehow, but the Enterprise doesn't have anything close to the weapons necessary."

"I'm the Head Tactician from the S.S Botany Bay." Mycroft introduced, "Give me a run down of all the weapons and their capacity on this ship, I will figure something out."

-oOo-

McCoy was surprised at how light Sherlock was considering the amount of muscle the warrior had on him. It was easy for he and John to get him back to the med bay, where a young woman with mousy hair was waiting for them looking very nervous.

"Molly." John greeted, "Words cannot express how happy I am to see you."

"What happened to Sherlock?" Molly gasped, taking in the burnt skin and hair.

"Radiation poisoning, let's get his vitals measured." McCoy supplied, "His skin isn't as bad as it was before, that's a good sign yes? Those super cells of his are working."

John bit his lip.

"Let's hope, the skin always heals first, to prevent infection, but it's his organs I'm worried about."

Molly proved an extraordinary asset in the Med Bay, despite her medical knowledge being several centuries out of date she was able to understand how almost everything worked. She poured over the history of radiation sickness and treatment on a data pad so fast that to McCoy the words were just blurs on the screen.

Meanwhile he and John hooked Sherlock up to a ventilator and took in his readings which were fluctuating wildly. With Sherlock's ever changing cells the machinery simply couldn't make heads or tails or the illness, one minute there was a cut in the skin the next it was healing then gone.

"His breathings weak." John muttered, "Add more oxygen to the mask. Twice normal."

"Do you do everything by double standards?" McCoy grumbled, John gave him a wry look.

"You should have seen the first time we decided to try alcohol, turns out we can really hold our drink."

"John, Sherlock's vitals are dropping!" Molly exclaimed.

Sherlock began to rasp and struggle for breath, despite the breathing mask. Joh turned white and McCoy quickly searched the computer for more treatments, Sherlock must have breathed in hot air filled with radiation when the core re-aligned.

"Come on, Sherlock." John begged quietly, holding his friends hand, "We didn't do all this just for you to give up now."

* * *

**Hey! Sorry about my slow uploads, but Im back at school now and doing 6 hours of study a day, plus classes and hanging out with my friends so writing is getting hard! I will try to update at least once a week or 10 days though.**


	9. Chapter 9

Kirk hurriedly tried to answer all of Mycroft and Irene's questions about modern starships, luckily Spock was there with every answer no mater how obscure. He was even able to recite the composition of dilithium crystals when Mycroft asked for it.

"These crystals are quite the oddity," Mycroft mused, far to calm for Kirk's mind, Moriarty would be on them soon enough.

"How many would you say Moriarty's ship would need to work?" Irene asked.

"Well, the Enterprise uses several, but Moriarty's ship is ten times the size, in order to warp as fast as us, he'd need hundreds." Kirk figured.

Mycroft got this sparkle in his eye that for some reason made Kirk nervous. It was a good thing they'd befriended Sherlock when they had. He didn't want this sharp minded man against him.

"If we could find a way on board his ship while the two fight, perhaps we could overload them." Mycroft decided, "It would cause a massive explosion and severe damage to his ship, more than likely killing him in the process. If the explosion didn't do the job the harsh environment of space certainly would. Even we're not that powerful."

"We can't beam somebody over without him knowing." Kirk argued to which Irene grinned.

"We don't have to beam, we can space surf as John calls it." She replied coyly.

"Space surf?" Spock questioned, if Kirk didn't know any better he'd have mistaken the Vulcan's tone for disbelief, even amusement.

"It's a great little game John, Sherlock and another one of us named Moran invented as children," Mycroft grinned, "It involves positioning to ships near each other and shooting people out the empty torpedo tubes wearing space suits."

"That's insane!" Kirk spluttered, "How would they not cream themselves on the other ships hull?"

"Well when they were younger they would simply have the other ship open their garbage disposal." Irene replied, "But in this case we're going to have to be more technical about it."

"Technical how?" Kirk asked suspiciously, he wasn't going to like this, he could tell.

"We will have to aim at Moriarty's own torpedo bays and time it just right so that John lands inside the empty bay. Then he can get out before the next missile is loaded."

"That is madness." Spock argued.

"Do you have a better plan?"

Kirk was sure he saw Spock's ears turn a darker shade of green.

-oOo-

"You want me to what?" John yelled, "I only just got Sherlock stable and you want me to leave him?"

"You're the only one whose ever gone space surfing here." Irene argued, "Moran is dead and Sherlock is in no condition to be fired out a torpedo bay!"

"Molly is here to watch over him as well as the ships doctors." Mycroft added, "It's only logical-"

"To hell with logical Mycroft." John fumed, "I am not going to shoot myself across space only to come back and find out Sherlock died because these hacks couldn't care for him properly."

"Oi!" McCoy scolded, "I'm not a hack! You're in my med bay, respect it!"

Mycroft opened his mouth to argue more but the ship was suddenly shaken by a huge tremor and Sherlock's monitors went haywire. John moved to go to him but Irene held him back while Molly and McCoy dealt with it aptly.

"See?"

John sighed.

"If I end up smeared across Moriarty's hull I'm going to haunt your arse."

-oOo-

It had been a long time since John had been in this position. Squeezed into a thin torpedo tube waiting to be blasted out into space. Last time he'd done this he hadn't been able to shave yet. The plan was deadly but he couldn't think of a better one. Kirk and Spock were keeping Moriarty busy with strategic dodging and distracting fire but it would only last so long.

John just prayed they got the timing right and he didn't end up being his with a blast from Moriarty's great black ship. Once he'd overloaded the crystals they would only have a few seconds to transport him out before the ship was crippled. Odds were not in his favour.

"Ready John?" Irene asked as his navigation screen switched on.

"As I'll ever be." He sighed.

"Firing in three...two...one..now!"

There was a sudden jolt the the Enterprise was suddenly behind him as John shot through the empty expanse of space. He glanced up above his where the laser fire from both ships was beginning to get heavy. He just had to pray none of it hit him.

"You need to angle yourself to the left another 21.5 degrees." Spock's calm voice ordered through his com, "The captain is going to release heavy fire on an area close to you now, you need to aim for the missile on the left near the bottom of the hull."

"Got it."

John silently thanked his younger self for doing this so he was prepared.

"You will hit the empty torpedo bay in exactly seventeen seconds."

"Wish me luck." John braced himself for impact, swinging his feet in front and blasting the thrusters to cushion the fall slightly.

"That would be illogical."

THUMP!

Even with the thrusters, hitting the back of the torpedo bay was brutal, a normal human would certainly have broken bones. Luckily, John wasn't a normal human and quickly he clambered out the hatch before the bay was reloaded.

"Are you aboard?" The Vulcan didn't even sound vaguely concerned.

"Yes, I'll find my way to the engines." John replied, "Let's hope this works."

-oOo-

Sherlock could feel himself coming into consciousness. The aches and burns were gone from his skin, meaning he was healed, outwardly at least. Yet, he still felt tired, extremely tired. If he wanted to he could let go and sink back down into sleep but he didn't allow himself the luxury.

With much more effort than he'd care to admit he forced his eyes open. That doctor, McCoy was looking down at him along with Molly. Molly was nervous and frivolous much of the time but Sherlock was glad to see her. She had always been especially loyal to him ever since he could remember, at least he had somebody he could trust in this weakened state.

"How long have I been out?" He asked, slowly sitting up, his muscled began to ache again.

"A hour or so." McCoy answered, "Your healing skills are living up to their name but you wont be fully healed for at least another day or so."

"The situation?" He asked, turning to Molly, she knew him well enough not to lie.

"We have a plan to cripple Moriarty's ship." She replied, "It's being executed as we speak, John space surfed over to the war ship to overload the engines-"

"You sent him alone?" Sherlock demanded, "Why? Irene is awake isn't she? Why not send her with him?"

He was usually John's partner in battle, but he hadn't been available. Now if John died because of him he'd just be another name to add to the already incredibly long list.

He was not going to let that happen.

* * *

**Sorry about the slow updates!**


	10. Chapter 10

"Sherlock you are not shooting yourself out a torpedo tube!" McCoy yelled.

Sherlock had been anything but a good patient since he woke. Despite being obviously weak to the point where two security guards could hold him back, Sherlock insisted on trying to follow John.

"The plan is terminally stupid!" He yelled, "I bet it was Mycroft's idea! He is always doing this!"

"John is already aboard Moriarty's vessel." McCoy replied, "It would be stupid for you to follow now, not only are you clearly injured and would most likely kill yourself getting over there, but by the time you got there John's mission would be close to over."

Sherlock hissed, getting up once more and wincing in obvious pain.

"Take me to the transport room then." He demanded, "I will be there when he beams back."

"You shouldn't be moving." Molly insisted but Sherlock shook her off when she tried to make him lie down.

"Kirk agreed to this plan?" Sherlock grumbled, stumbling a bit as he walked out of the med bay.

Molly nodded.

"I will have to reevaluate him." Sherlock muttered.

Molly followed along behind him nervously, she knew she should have sedated him...

Instead of heading to the transport room, Sherlock instead walked back toward the deck of the ship. The pace was slow due to Sherlock breathing hard after only a minute of walking and the ships continued tremors from torpedo hits. Molly had a feeling her friend was too embarrassed to mention he didn't remember the way to the transporter room. So instead he was just going to where he thought Mycroft would be.

"Sherlock this isn't a good idea you're still-"

"Recovering, yes yes, do tire somebody else with your mother duck routine today Molly." He snapped.

The deck door opened with a quiet whoosh, revealing a chaotic scene. People were yelling at all stations, firing, keeping shields up, maintaining speed and all manner of things Molly had never been trained to understand.

"Mycroft!" Sherlock bellowed, spotting both he and Irene standing either side of Kirk discussing strategies. Molly couldn't help but notice the small smile that passed over Sherlock's face when he noticed Kirks obvious discomfort at being told what to do.

"Now isn't the best time Sherlock." Kirk replied before Mycrfot could, "shouldn't you be-?"

"Enough of that! Mycroft how could you do this to John?" Sherlock demanded, he opened his mouth to say more but was thrown heavily against the back of the captains chair as the ship swerved.

"Hull breach in section 14 captain!" Sulu yelled.

"Storage." Kirk explained briefly to the confused super humans, "could be worse, what is taking John so long?"

The captain hit the intercom.

"Bridge to Spock."

"Spock here." Came the slightly static voice.

"Is John done yet we can't hold out much longer."

"He is yet to communicate his wish to transport back."

Sherlock scowled.

"Which way to the transporter room from here?" He demanded.

"Level four." Kirk replied, instantly refocusing on ordering the ships manoeuvres, clearly he didn't have time to argue with Sherlock and Molly was thankful.

"We will be talking about this later Mycroft." Sherlock hissed before turning and heading back out the door to the transporter room, leaving Molly feeling bewildered. He never could stay in one place very long could he. She was tempted to try and make him return to sick bay but decided not to waste her breath. Instead she simply followed him out and prayed Moriarty's aim would worsen.

-oOo-

On reflection, John decided, he should have asked how exactly one goes about overloading dilithium crystals. It hasn't been hard to find his way to where the engines worked, Moriarty's was obviously trying to have as little crew as possible, taking full advantage of a one man war ship for which John was extremely thankful.

The crystals seemed to be focusing energy I to the engines that allowed for the amazing warp speed, but he could hardly just rip them out, not if he wanted some unfried brain left.

"When in doubt press all the buttons." He sighed and immediately began to fiddle with every button, dial and switch he could find.

It didn't take him long to discover that if he pushed every dial to maximum the crystals began to spark and flare inside the engines, causing the many coloured bars measuring the power and pressure inside the chambers to rise.

"Spock this is John beam me over, this place is about to blow sky high." He called after turned all the dials up.

"That statement is redundant as we are in space and there is no-"

"Is this really the time?" John snapped as smoke began to pour into the room, "beam me up!"

John felt his heart begin to race as he waited for the light of the transporter to appear but failed. The engines were sparking now and the machinery was going into overload.

"John!"

"Sherlock?"

What was he doing out of bed?

"The residual energy from the overloading crystals is making it hard to lock onto you." Sherlock explained with concern in his voice, "stay still, this could take a moment..."

John didn't mention that he had very few of those and instead did his best not to move too much as sparks began to rain down on him. The engines began to glow...

"Engage!"

BOOM!

* * *

**Sorry this is so late! Only one or two chapters left though :)**


	11. Chapter 11

John flopped down onto the ground with relief as he materialised in the transport room. His body stung from several shallow cuts and burns where the transport has failed to teleport sections of skin but he didn't care. He was too busy enjoying the sensation of breathing, it was so under appreciated.

"John?"

Sherlock was kneeling in front of him with concern in his eyes. Of course he was trying his best to hide it from the star fleet crewmen in the room with them. John sighed in relief, graphing Sherlock's shoulder to assure him he was fine, he was still too winded and shocked to speak. His friend returned the gesture.

"You are quite unharmed." Spooked noted, "The transporter managed to pick up 99.998% of your signal. Those cuts should be the only effects."

"So the ship is gone?" John questioned as Sherlock helped him to his feet.

"Yes and to our understanding Moriarty with it."Sherlock replied before swaying slightly, instantly activating John's doctor mode.

"You should be resting." He scolded, "come on, back to the med bay with you."

Sock gave them a nod and when to assist with the patching where the torpedoes had managed to breach. John couldn't believe a hull breach wasn't a death sentence anymore, Sherlock began to explain invisible force field patching and some other form of repair that made no sense to his doctor but he let him prattle along anyway.

He couldn't help but feel uneasy. It just seemed...too easy.

-oOo-

Now that the imminent threat was gone Sherlock was a much more agreeable patient, he still wasn't a good patient though. But at least he stayed in bed, for the most part.

"We will be sending a recon team to gather up the debris and find the body." Kirk informed them before turning to John, "thank you, for saving my ship and my crew."

"I never thought I'd say this to a Starfleet officer but, you're welcome." John replied with a smile, "you're not half bad really."

"I'm sorry to break up this happy chat." Mycroft cut in.

"No you're not." Sherlock scoffed, Irene shot him a look.

"Anyway." Mycroft continued, "Has nobody though about what we will do when we reach Earth? We may not be so welcome."

Sherlock and John's faces became serious, they were right, nobody had thought of that.

"With the Admiral gone there is nobody left to condemn you." Kirk argued, "If we explain to Starfleet maybe you could come join us on the enterprise. We could always use keen strategists and those engineers you've got are brilliant."

Sherlock made a face.

"I don't like running bout space myself." Mycroft replied, "however the administration at your new and more modern Starfleet could certainly use my expertise..."

"He'll be running the place in a few years." John groaned, Sherlock chuckled.

"Indeed, I would much like to hear more of those strategise you have created." Spock noted, Sherlock rolled his eyes.

"I don't think I will look particularly good in Starfleet uniform captain." Sherlock decided, "and I don't think John would take to it either somehow. I've seen enough of your new Starfleet to last me a life time. Though I imagine Anderson and Donovan will revel in being the brightest bulbs in the room for once, they'll join you. They never did much like listening to me."

"So what will you do?" Spock asked.

"Oh we'll figure something out."

-oOo-

Sherlock was right, Anderson and Donovan jumped at the chance to be experts at something for once and were practically running the engineering workshops on Earth in a matter of days, making modifications to the Starships.

Irene managed, somehow, to get a ship of her own. Kirk had a sneaking suspicion it had something to do with the numerous members of higher up Officials that came to work with thick scarves wrapped around their necks over the coming weeks, despite the fact it was the height of summer.

Lestrade as it turned out quite liked the Enterprise and stayed on, Kirk found himself enjoying the mans company immensely. Even if he was unusually good at cards and more than a little sarcastic. Spock said he talked too much but Bones as always, disagreed and spent almost every spare moment drinking with the man.

Sherlock and John however, slipped off the ship as soon as they docked and disappeared completely. Molly, who was staying on as McCoy's second in command, seemed to know something but wasn't letting on for even a second but Kirk didn't worry. He was a little sad he never got to say goodbye though, they really were two very extraordinary beings, even for super humans.

It took months to pick up all the remains of the warship and while they recovered body after body, none were Moriarty. The investigation ruled that he must have been completely destroyed in the blast but Kirk couldn't help but feel he was still out there...

"Captain, we're waiting for your order."

Spock snapped him out of his daydreams. It had been several months now, since Sherlock and John had vanished and the Enterprise was finally ready to redeploy.

"Oh right, engage." He ordered, smiling contently as the ship rocketed off into warp.

They had only been traveling for a few minutes before Spock announced, with as much surprise as a Vulcan could, that they had a message.

Who could be messaging them already? Surely it couldn't already be a distress call, they were only a few miles out of the galaxy.

"On screen."

"Hello Kirk!"

John's beaming face filled the screen and Jim felt himself laugh.

"Sorry about slipping away like we did but if we hadn't wed have never gotten away without a lot of fuss. And you know us, we like a quiet life."

That last line was dripping with sarcasm.

"Anyway, we've managed to 'acquire' a small ship for the two of us and were actually pretty happy it's not as fancy as yours obviously but-

A loud growling sound echoed behind the doctor and he turned, making a face of exasperation to something off screen.

"Sherlock I told you not to bring strange creatures up from the planets we visit!"

John shook his head and rolled his eyes before becoming serious.

"Anyway, look, we both know you didn't find Moriarty's body and that he is considered dead but were not going to take that chance. We're going looking for him, all over space if we have to. Don't try and find us, because you never will but if you need us, or find something that could be Moriarty's work, send us a message in reply t this one. We will get back to you."

Kirk found himself nodding, even though the message was prerecorded.

"Well, till next time." John smiled and gave a mock salute before the message ended.

"Something tells me we will be seeing those two again." Lestrade sighed.

"You know what?" Kirk grinned, "So do I."

* * *

**I left the end a little ambiguous in case I have the time to write a sequel. Thanks for sticking with this story I'm glad you enjoyed it or at least I hope you did**!


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